Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 31 of 106
Found at i:5776321 original size:24 final size:23
Alignment explanation
Indices: 5776288--5776343 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
5776278 TCTTTTCTTC
* * *
5776288 TTTTTCTTTCTTTCTTTCTTTGTT
1 TTTTTTTTTCATTCTTTCATT-TT
5776312 TTTTTTTTTCATTCTTTCATTTT
1 TTTTTTTTTCATTCTTTCATTTT
*
5776335 TTTCTTTTT
1 TTTTTTTTT
5776344 GTCCTTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTTTTTTCATTCTTTCATTTT
Found at i:5781190 original size:6 final size:6
Alignment explanation
Indices: 5781173--5781207 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5781163 ATCTAACAAG
*
5781173 TGAGGT TAAGGT TGAGGT TGAGGT TGAGGT TGAGG
1 TGAGGT TGAGGT TGAGGT TGAGGT TGAGGT TGAGG
5781208 AGGATGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.49, T:0.31
Consensus pattern (6 bp):
TGAGGT
Found at i:5781304 original size:23 final size:25
Alignment explanation
Indices: 5781278--5781329 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
5781268 TTAAGTATAA
5781278 AAAT-TTTAATTTTT-TATTGA-TAT
1 AAATGTTT-ATTTTTGTATTGATTAT
5781301 AAATGTTTATTTTTGTATTGATTAT
1 AAATGTTTATTTTTGTATTGATTAT
5781326 AAAT
1 AAAT
5781330 CTTGATGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.38
24 9 0.35
25 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (25 bp):
AAATGTTTATTTTTGTATTGATTAT
Found at i:5781314 original size:24 final size:24
Alignment explanation
Indices: 5781278--5781329 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5781268 TTAAGTATAA
*
5781278 AAATTTTAATTTTTTATTGA-TAT
1 AAATTTTAATTTTGTATTGATTAT
*
5781301 AAATGTTTATTTTTGTATTGATTAT
1 AAAT-TTTAATTTTGTATTGATTAT
5781326 AAAT
1 AAAT
5781330 CTTGATGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 14 0.56
25 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (24 bp):
AAATTTTAATTTTGTATTGATTAT
Found at i:5783270 original size:3 final size:3
Alignment explanation
Indices: 5783262--5783309 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5783252 ATCAAACATG
5783262 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5783310 GCAAAAAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5784823 original size:162 final size:160
Alignment explanation
Indices: 5784622--5785212 Score: 573
Period size: 162 Copynumber: 3.7 Consensus size: 160
5784612 AGTAAGTTAA
* * * *
5784622 GCATGAGAAAAGTTGCAGTTTATGTATTTTTAGCACTTTTTGTGACATAAAAGGGAAAAAATGTA
1 GCATGAAAAAAGTTTCAGTTTATGTGTTTTTAGCACTTTTTGTGCCATAAAAGGG-AAAAATGTA
* * *
5784687 AATTTGCTACTATAATTATGCTTTAACAACTTACATAGCTTGAATACATGATATTAAACTTATCT
65 AATTTGCTACTATAATTATGTTTTAACAACTTAGATAGCTTGAATACATGATATTAAACTTGTCT
* **
5784752 GAATGTTTGAGCTTGATTGCCACACTTGATAT
130 GAATGTTT-AGCTTGGTTGCCATGCTTGATAT
* * * *
5784784 GCATGAAAAAAGTTTCAGTTTATGTGTTTCTATCACTTTTAGTGCCGTAAAAGGGCAAAAATGTA
1 GCATGAAAAAAGTTTCAGTTTATGTGTTTTTAGCACTTTTTGTGCCATAAAAGGG-AAAAATGTA
* * * * * *
5784849 AATTTGTTGCTATCATTTTGTTTTAACAACATAGATTGCTTGAATACATGATATTAAACTTGT-T
65 AATTTGCTACTATAATTATGTTTTAACAACTTAGATAGCTTGAATACATGATATTAAACTTGTCT
* * * *
5784913 CAAATGATTAAACTTGGTTGCCATGCTTAATAT
130 -GAATG-TTTAGCTTGGTTGCCATGCTTGATAT
* * * * * * *
5784946 --ATGTGAAAATGTTATGA-TTTATGTGTTTTTAGGACTTTATT-TGCCATAAAAAGGTAGATAT
1 GCATG-AAAAAAGTT-TCAGTTTATGTGTTTTTAGCACTTT-TTGTGCCAT-AAAAGGGAAAAAT
* * * * * **
5785007 GTAAATTTGCTACTATATTTTTGTTTTAATAATTTAGATAACTCAAATACATGATATTAAACTTG
62 GTAAATTTGCTACTATAATTATGTTTTAACAACTTAGATAGCTTGAATACATGATATTAAACTTG
* * * *
5785072 TCTGATTATTTACGCTTGGCTACCATGCTTGATAT
127 TCTGAATGTTTA-GCTTGGTTGCCATGCTTGATAT
* * ***
5785107 GGATGAAAAAAGTTAC-GATTTATGTGTTTTTAGCACTTTTTGTGTTGTGAAAAGGGAAAAATGT
1 GCATGAAAAAAGTTTCAG-TTTATGTGTTTTTAGCACTTTTTGTGCCAT-AAAAGGGAAAAATGT
* * * *
5785171 AAATTTGTTGCTATAATTATGTTTTATCAGCTTAGATAGCTT
64 AAATTTGCTACTATAATTATGTTTTAACAACTTAGATAGCTT
5785213 AGATATCTCA
Statistics
Matches: 339, Mismatches: 77, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
160 6 0.02
161 112 0.33
162 216 0.64
163 5 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (160 bp):
GCATGAAAAAAGTTTCAGTTTATGTGTTTTTAGCACTTTTTGTGCCATAAAAGGGAAAAATGTAA
ATTTGCTACTATAATTATGTTTTAACAACTTAGATAGCTTGAATACATGATATTAAACTTGTCTG
AATGTTTAGCTTGGTTGCCATGCTTGATAT
Found at i:5791044 original size:21 final size:21
Alignment explanation
Indices: 5791011--5791053 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5791001 TGTAAGCATC
*
5791011 AGTGTATACTCCTAACGAAAA
1 AGTGCATACTCCTAACGAAAA
* *
5791032 AGTGCATAGTCCTAATGAAAA
1 AGTGCATACTCCTAACGAAAA
5791053 A
1 A
5791054 ATGGCAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (21 bp):
AGTGCATACTCCTAACGAAAA
Found at i:5794831 original size:53 final size:53
Alignment explanation
Indices: 5794727--5794831 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
5794717 TAATTAATGA
* * *
5794727 ATTTATTTTCACTTTTAGCTGTGTTTATAAAATTCTATTTTCTTATGGTGCTC
1 ATTTATTTTCACTCTTAGATGTGTTTATAAAATTCTATTTTCTTATAGTGCTC
*
5794780 ATTTATTTTCACTCTTAGATGTGTTTATAAAA-TCTTATTTTCTTGTAGTGCT
1 ATTTATTTTCACTCTTAGATGTGTTTATAAAATTC-TATTTTCTTATAGTGCT
5794832 TTTAGGCAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
52 2 0.04
53 45 0.96
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.54
Consensus pattern (53 bp):
ATTTATTTTCACTCTTAGATGTGTTTATAAAATTCTATTTTCTTATAGTGCTC
Found at i:5800751 original size:12 final size:13
Alignment explanation
Indices: 5800734--5800763 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5800724 TTATACTATA
5800734 ACAAAA-AAAATT
1 ACAAAATAAAATT
5800746 ACAAAATAAAATT
1 ACAAAATAAAATT
5800759 ACAAA
1 ACAAA
5800764 TTTTACTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (13 bp):
ACAAAATAAAATT
Found at i:5806298 original size:14 final size:14
Alignment explanation
Indices: 5806279--5806315 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5806269 ACAATTTCTT
*
5806279 AAACACTAATATAA
1 AAACACCAATATAA
5806293 AAACACCAATATAA
1 AAACACCAATATAA
*
5806307 AAACCCCAA
1 AAACACCAA
5806316 ACCAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (14 bp):
AAACACCAATATAA
Found at i:5807925 original size:25 final size:25
Alignment explanation
Indices: 5807891--5807940 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5807881 TGTAATCCTC
5807891 GAATTATCATCCGCAAATATATCTT
1 GAATTATCATCCGCAAATATATCTT
5807916 GAATTATCATCCGCAAATATATCTT
1 GAATTATCATCCGCAAATATATCTT
5807941 ATGCCAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (25 bp):
GAATTATCATCCGCAAATATATCTT
Found at i:5811323 original size:3 final size:3
Alignment explanation
Indices: 5811315--5811347 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
5811305 CAAAACTCAT
5811315 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA
5811348 GGGAAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5811337 original size:16 final size:16
Alignment explanation
Indices: 5811316--5811347 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5811306 AAAACTCATT
5811316 AATAATAATAATAATA
1 AATAATAATAATAATA
5811332 AATAATAATAATAATA
1 AATAATAATAATAATA
5811348 GGGAAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:5817069 original size:12 final size:12
Alignment explanation
Indices: 5817049--5817093 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5817039 TGTTAAATAC
5817049 CAAAAAAACAAA
1 CAAAAAAACAAA
*
5817061 CAAACAAACAAA
1 CAAAAAAACAAA
* *
5817073 TAAAAAATAAAAA
1 CAAAAAA-ACAAA
5817086 CAAAAAAA
1 CAAAAAAA
5817094 GAAGAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.04
Consensus pattern (12 bp):
CAAAAAAACAAA
Found at i:5817574 original size:11 final size:11
Alignment explanation
Indices: 5817558--5817588 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5817548 TGAAAGGATG
5817558 AAAAAAAAAAC
1 AAAAAAAAAAC
*
5817569 AAAAAAAAAAT
1 AAAAAAAAAAC
5817580 AAAAAAAAA
1 AAAAAAAAA
5817589 GAAATGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.94, C:0.03, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:5818691 original size:43 final size:43
Alignment explanation
Indices: 5818638--5818759 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
5818628 ACATGTGCAT
* * * *
5818638 CATGAGAAAGATATTTGCATTTACATCACTTGCATCTGTATCA
1 CATGAAAAAGACATTTGCATTTACATCACTTGCATCGGCATCA
*
5818681 CATGAAAAAGACATTTGCATTTACATCATTTGCATCGGCATCA
1 CATGAAAAAGACATTTGCATTTACATCACTTGCATCGGCATCA
* * * * *
5818724 TAAGAAAAAAGGCATTTGCATTTGCATCGCTTGCAT
1 CATG-AAAAAGACATTTGCATTTACATCACTTGCAT
5818760 TTACATCATG
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 40 0.60
44 27 0.40
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (43 bp):
CATGAAAAAGACATTTGCATTTACATCACTTGCATCGGCATCA
Found at i:5820089 original size:76 final size:74
Alignment explanation
Indices: 5820002--5820194 Score: 196
Period size: 73 Copynumber: 2.6 Consensus size: 74
5819992 AAAGATTTTT
* * *
5820002 TTTTTTAAGTTTTAAAGCCT-TAATTT-GTGGAGAGCTATTTTCAAAAAGTTTCAAAGTCTCCAT
1 TTTTTAAAGTTTCAAAGCCTCT-ATTTAG-GGAGAGCTATTTTC--AAAGTTTCAAAGCCTCCAT
5820065 TTGGGGAAAGCCA
62 TTGGGGAAAGCCA
* * * *
5820078 TTTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCTATTTTCAAAGTTTCAAGGCCTCTATTTGG
1 TTTTTAAAGTTTCAAAGCCTCTATTTAGGGAGAGCTATTTTCAAAGTTTCAAAGCCTCCATTTGG
* *
5820143 GG-GAGCAA
66 GGAAAGCCA
* * * *
5820151 CTTTTT-AAGTTTCATAGCCTCTATTTGGGGTGAGCAATTTTCAA
1 -TTTTTAAAGTTTCAAAGCCTCTATTTAGGGAGAGCTATTTTCAA
5820195 TCAAGTTGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
73 37 0.37
74 27 0.27
76 34 0.34
77 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (74 bp):
TTTTTAAAGTTTCAAAGCCTCTATTTAGGGAGAGCTATTTTCAAAGTTTCAAAGCCTCCATTTGG
GGAAAGCCA
Found at i:5820092 original size:37 final size:36
Alignment explanation
Indices: 5820002--5820191 Score: 168
Period size: 37 Copynumber: 5.1 Consensus size: 36
5819992 AAAGATTTTT
* * * *
5820002 TTTTTTAAGTTTTAAAGCCT-TAATTTGTGGAGAGCTA
1 TTTTTAAAGTTTCAAAGCCTCT-ATTTG-GGGGAGCAA
* * * * *
5820039 TTTTCAAAAAGTTTCAAAGTCTCCATTTGGGGAAAGCCA
1 TTTT--TAAAGTTTCAAAGCCTCTATTTGGGG-GAGCAA
* *
5820078 TTTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCTA
1 TTTTTAAAGTTTCAAAGCCTCTATTT-GGGGGAGCAA
* *
5820115 TTTTCAAAGTTTCAAGGCCTCTATTTGGGGGAGCAA
1 TTTTTAAAGTTTCAAAGCCTCTATTTGGGGGAGCAA
*
5820151 CTTTTT-AAGTTTCATAGCCTCTATTTGGGGTGAGCAA
1 -TTTTTAAAGTTTCAAAGCCTCTATTTGGGG-GAGCAA
5820188 TTTT
1 TTTT
5820192 CAATCAAGTT
Statistics
Matches: 125, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
36 35 0.28
37 59 0.47
38 6 0.05
39 25 0.20
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (36 bp):
TTTTTAAAGTTTCAAAGCCTCTATTTGGGGGAGCAA
Found at i:5821027 original size:144 final size:144
Alignment explanation
Indices: 5820693--5821090 Score: 518
Period size: 144 Copynumber: 2.8 Consensus size: 144
5820683 GAGAAGTATA
* * * *
5820693 AAATTACCAAGATACCCTTATAAGGATATTTTCGTAATTTGACATT-TTCGAGCTCAAATTGTCA
1 AAATTACCAAAATACCC-TATAAGGATATTTTTGTAATTTGACCTTCTT-GAGCTCAAATTTTCA
* * * *
5820757 TGAAACTTTTTAGATCTTAATTTCATAATATTTCATGA--TTTGTTGCATTTGAAATCGCAGTCA
64 TGAAAATTTTTAGATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAGACA
*
5820820 TACCCTGAGAAGTGTG
129 TACCCTGAGAAATGTG
* * * *
5820836 AAATTACCAAAATACCCCTTTAAGGTTAATTTTGTAATTTGACCTTCTTAAGCTCAAATTTTCAT
1 AAATTACCAAAATA-CCCTATAAGGATATTTTTGTAATTTGACCTTCTTGAGCTCAAATTTTCAT
* * *
5820901 GAAAATTTTCAGATCTTAATGTCATAATATTTCATGATTTTTGGTGCATTTGAAATCATA-ACAG
65 GAAAATTTTTAGATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAGACA-
5820965 TA-CCTGAGAAATGTG
129 TACCCTGAGAAATGTG
* *
5820980 AAATTACCAAAATACCTCTATAAGGGTATTTTTGTAATTTGACCTTCTCGAGCTCAAATTTTCAT
1 AAATTACCAAAATACC-CTATAAGGATATTTTTGTAATTTGACCTTCTTGAGCTCAAATTTTCAT
* * * *
5821045 GAAAATTTTTAAATCTCAATTTTATAATATTTTATGATTTTTGGTG
65 GAAAATTTTTAGATCTTAATTTCATAATATTTCATGATTTTTGGTG
5821091 TTTTAAAATC
Statistics
Matches: 222, Mismatches: 27, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
143 86 0.39
144 116 0.52
145 20 0.09
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (144 bp):
AAATTACCAAAATACCCTATAAGGATATTTTTGTAATTTGACCTTCTTGAGCTCAAATTTTCATG
AAAATTTTTAGATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAGACATA
CCCTGAGAAATGTG
Found at i:5824723 original size:37 final size:38
Alignment explanation
Indices: 5824668--5824912 Score: 225
Period size: 37 Copynumber: 6.5 Consensus size: 38
5824658 TGTGCATGAG
* *
5824668 ATGCATGTACTA-CTTATTAAGATGTGCACAAGATGGA
1 ATGCATGTACTATCTTATTAAGATATGCATAAGATGGA
* *
5824705 ATGCATGTACTATC-TATTAAGATATGCATGAGAT-AA
1 ATGCATGTACTATCTTATTAAGATATGCATAAGATGGA
* * * * * **
5824741 AGTACATGTATTAT-TTATTAAGATGTGTATGAGATATA
1 A-TGCATGTACTATCTTATTAAGATATGCATAAGATGGA
* * * *
5824779 ATGCATGTTCTTATCTTATTAAAATGTGCATAGGATGGA
1 ATGCATGTAC-TATCTTATTAAGATATGCATAAGATGGA
* * * *
5824818 ATGTATGTACTAT-ATATTAAGATATGTATATGATGGA
1 ATGCATGTACTATCTTATTAAGATATGCATAAGATGGA
*
5824855 GTGCATGTACTTATCTTATTAAGATATGCATGAA-ATGGA
1 ATGCATGTAC-TATCTTATTAAGATATGCAT-AAGATGGA
5824894 ATG-ATGTACTATCTTATTA
1 ATGCATGTACTATCTTATTA
5824913 TTTCCAACTT
Statistics
Matches: 168, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
36 2 0.01
37 100 0.60
38 18 0.11
39 47 0.28
40 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (38 bp):
ATGCATGTACTATCTTATTAAGATATGCATAAGATGGA
Found at i:5824842 original size:113 final size:113
Alignment explanation
Indices: 5824668--5824912 Score: 291
Period size: 113 Copynumber: 2.2 Consensus size: 113
5824658 TGTGCATGAG
* *
5824668 ATGCATGTACTACTTATTAAGATGTGCACAAGATGGAATGCATGTACTATCTATTAAGATATGCA
1 ATGCATGTACTACTTATTAAAATGTGCACAAGATGGAATGCATGTACTATATATTAAGATATGCA
5824733 TGA-GATAAAGTACATGTA-TTAT-TTATTAAGATGTGTATGAGATATA
66 T-ATGATAAAGTACATGTACTTATCTTATTAAGATGTGTATGAGATATA
* * * *
5824779 ATGCATGTTCTTATCTTATTAAAATGTGCATAGGATGGAATGTATGTACTATATATTAAGATATG
1 ATGCATGTAC-TA-CTTATTAAAATGTGCACAAGATGGAATGCATGTACTATATATTAAGATATG
* ** * * * * **
5824844 TATATGATGGAGTGCATGTACTTATCTTATTAAGATATGCATGAAATGGA
64 CATATGATAAAGTACATGTACTTATCTTATTAAGATGTGTATGAGATATA
5824894 ATG-ATGTACTATCTTATTA
1 ATGCATGTACTA-CTTATTA
5824913 TTTCCAACTT
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
111 9 0.08
112 3 0.03
113 70 0.62
114 9 0.08
115 22 0.19
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (113 bp):
ATGCATGTACTACTTATTAAAATGTGCACAAGATGGAATGCATGTACTATATATTAAGATATGCA
TATGATAAAGTACATGTACTTATCTTATTAAGATGTGTATGAGATATA
Found at i:5824912 original size:76 final size:74
Alignment explanation
Indices: 5824672--5824912 Score: 247
Period size: 76 Copynumber: 3.2 Consensus size: 74
5824662 CATGAGATGC
* * *
5824672 ATGTACTACTTATTAAGATGTGCACAAGATGGAATGCATGTAC-TATC-TATTAAGATATGCATG
1 ATGTACTATTTATTAAGATGTGTA-TAGATGGAATGCATGTACTTATCTTATTAAGATATGCATG
* *
5824735 AGAT-AAAGTAC
65 AGATGGAA-T-G
* ** * * *
5824746 ATGTATTATTTATTAAGATGTGTATGAGATATAATGCATGTTCTTATCTTATTAAAATGTGCAT-
1 ATGTACTATTTATTAAGATGTGTAT-AGATGGAATGCATGTACTTATCTTATTAAGATATGCATG
5824810 AGGATGGAATG
65 A-GATGGAATG
* * *
5824821 TATGTACTATATATTAAGATATGTATATGATGGAGTGCATGTACTTATCTTATTAAGATATGCAT
1 -ATGTACTATTTATTAAGATGTGTATA-GATGGAATGCATGTACTTATCTTATTAAGATATGCAT
*
5824886 GAAATGGAATG
64 GAGATGGAATG
5824897 ATGTACTATCTTATTA
1 ATGTACTAT-TTATTA
5824913 TTTCCAACTT
Statistics
Matches: 136, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
74 35 0.26
75 15 0.11
76 83 0.61
77 3 0.02
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (74 bp):
ATGTACTATTTATTAAGATGTGTATAGATGGAATGCATGTACTTATCTTATTAAGATATGCATGA
GATGGAATG
Found at i:5828380 original size:33 final size:35
Alignment explanation
Indices: 5828333--5828407 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
5828323 AAAAAAATCC
5828333 TATAAAAAATCATGC-AAAGA-TATCAAGCAATAAA
1 TATAAAAAATCATGCTAAA-ATTATCAAGCAATAAA
*
5828367 TATAAAAAA-CATGCTAAAATTATCATGCAATAAA
1 TATAAAAAATCATGCTAAAATTATCAAGCAATAAA
5828401 TAGTAAA
1 TA-TAAA
5828408 TCATGCAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 6 0.16
34 27 0.73
35 4 0.11
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.24
Consensus pattern (35 bp):
TATAAAAAATCATGCTAAAATTATCAAGCAATAAA
Found at i:5828476 original size:16 final size:16
Alignment explanation
Indices: 5828457--5828504 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5828447 AATAAACATG
5828457 CAAATAAATAATAAAT
1 CAAATAAATAATAAAT
*
5828473 CAAATATATAA-ATAAT
1 CAAATAAATAATA-AAT
**
5828489 CATGTAAATAATAAAT
1 CAAATAAATAATAAAT
5828505 AATGATGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (16 bp):
CAAATAAATAATAAAT
Found at i:5828528 original size:22 final size:21
Alignment explanation
Indices: 5828500--5828550 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
5828490 ATGTAAATAA
* *
5828500 TAAATAATGATGCAAGAATAAAT
1 TAAATAATCAAGCAA-AA-AAAT
5828523 T-AATAATCAAGCAAAAAAAT
1 TAAATAATCAAGCAAAAAAAT
5828543 TAAATAAT
1 TAAATAAT
5828551 AAATAAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 5 0.20
21 8 0.32
22 11 0.44
23 1 0.04
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (21 bp):
TAAATAATCAAGCAAAAAAAT
Found at i:5831839 original size:18 final size:17
Alignment explanation
Indices: 5831805--5831845 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
5831795 CAATTCTCTC
* *
5831805 TTCTTTTTTTTTTTGTT
1 TTCTTTTTTTATATGTT
5831822 TTCTTTCTTTTATATGTT
1 TTCTTT-TTTTATATGTT
5831840 TTCTTT
1 TTCTTT
5831846 GATTTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (17 bp):
TTCTTTTTTTATATGTT
Found at i:5836522 original size:40 final size:39
Alignment explanation
Indices: 5836440--5836556 Score: 128
Period size: 40 Copynumber: 3.0 Consensus size: 39
5836430 AAGCATAGGG
* * * *
5836440 TTTGCCTGGAAGCCTTGAAAATTATTCAAAAATCTACGGT
1 TTTGCCTGGAGGCCTTGGAAATCATTCAAAAATCTA-AGT
* *
5836480 TTTGCCCGGAGGCCTTGGGAATCATTCAAAAATCCTAAGT
1 TTTGCCTGGAGGCCTTGGAAATCATTCAAAAAT-CTAAGT
** *
5836520 TTT-CCTATAGGCCTTGGAAATCATTCGAAAATCTAAG
1 TTTGCCTGGAGGCCTTGGAAATCATTCAAAAATCTAAG
5836557 GTTCTACCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 5 0.08
39 24 0.37
40 33 0.51
41 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (39 bp):
TTTGCCTGGAGGCCTTGGAAATCATTCAAAAATCTAAGT
Found at i:5836543 original size:39 final size:40
Alignment explanation
Indices: 5836451--5836591 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
5836441 TTGCCTGGAA
* * * * * ***
5836451 GCCTTGAAAATTATTCAAAAATCTACGGTTTTGCCCGGAG
1 GCCTTGGAAATCATTCAAAAATCTAAGGTTCTACCTAAAG
* * *
5836491 GCCTTGGGAATCATTCAAAAATCCTAA-GTT-TTCCTATAG
1 GCCTTGGAAATCATTCAAAAAT-CTAAGGTTCTACCTAAAG
*
5836530 GCCTTGGAAATCATTCGAAAATCTAAGGTTCTACCTAAAG
1 GCCTTGGAAATCATTCAAAAATCTAAGGTTCTACCTAAAG
* *
5836570 GTCTT-GAAATTCTTTCAAAAAT
1 GCCTTGGAAA-TCATTCAAAAAT
5836592 TTAAAATTCT
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
38 4 0.05
39 32 0.39
40 43 0.52
41 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (40 bp):
GCCTTGGAAATCATTCAAAAATCTAAGGTTCTACCTAAAG
Found at i:5836591 original size:40 final size:39
Alignment explanation
Indices: 5836489--5836591 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 39
5836479 TTTTGCCCGG
* * *
5836489 AGGCCTTGGGAATCATTCAAAAATCCTAAGTTTTCCTAT
1 AGGCCTTGGAAATCATTCAAAAATCCTAAGTTTACCTAA
*
5836528 AGGCCTTGGAAATCATTCGAAAAT-CTAAGGTTCTACCTAA
1 AGGCCTTGGAAATCATTCAAAAATCCTAA-GTT-TACCTAA
* *
5836568 AGGTCTT-GAAATTCTTTCAAAAAT
1 AGGCCTTGGAAA-TCATTCAAAAAT
5836592 TTAAAATTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
38 4 0.07
39 29 0.54
40 21 0.39
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (39 bp):
AGGCCTTGGAAATCATTCAAAAATCCTAAGTTTACCTAA
Found at i:5836691 original size:21 final size:22
Alignment explanation
Indices: 5836667--5836710 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5836657 AATTTTTCAA
5836667 TTTCTAAA-TTTT-CACCTTTTG
1 TTTC-AAAGTTTTCCACCTTTTG
*
5836688 TTTCAAAGTTTTCCACTTTTTG
1 TTTCAAAGTTTTCCACCTTTTG
5836710 T
1 T
5836711 GCCAAGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 9 0.45
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTCAAAGTTTTCCACCTTTTG
Found at i:5838535 original size:112 final size:112
Alignment explanation
Indices: 5838338--5838561 Score: 439
Period size: 112 Copynumber: 2.0 Consensus size: 112
5838328 TATTAATTTT
5838338 TATTATTTTATATTCTTATATTTGTTATTTTATTAGAACAAATTTATTTTAAGTTACGAAAATGT
1 TATTATTTTATATTCTTATATTTGTTATTTTATTAGAACAAATTTATTTTAAGTTACGAAAATGT
5838403 ATGAAAATTCTTAATGAATAAAATTTCCTAAATACCCCATTATCTAG
66 ATGAAAATTCTTAATGAATAAAATTTCCTAAATACCCCATTATCTAG
5838450 TATTATTTTATATTCTTATATTTGTTATTTTATTAGAACAAATTTATTTTAAGTTACGAAAATGT
1 TATTATTTTATATTCTTATATTTGTTATTTTATTAGAACAAATTTATTTTAAGTTACGAAAATGT
*
5838515 ATGAAAATTCTTAATGAATAAAATTTTCTAAATACCCCATTATCTAG
66 ATGAAAATTCTTAATGAATAAAATTTCCTAAATACCCCATTATCTAG
5838562 GCAGCATTTG
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (112 bp):
TATTATTTTATATTCTTATATTTGTTATTTTATTAGAACAAATTTATTTTAAGTTACGAAAATGT
ATGAAAATTCTTAATGAATAAAATTTCCTAAATACCCCATTATCTAG
Found at i:5838766 original size:13 final size:13
Alignment explanation
Indices: 5838750--5838818 Score: 75
Period size: 13 Copynumber: 5.3 Consensus size: 13
5838740 GGGCTTGGAT
*
5838750 TTTAGGGTTCCAA
1 TTTAGGGTTTCAA
*
5838763 TTTAGGGTTTTAA
1 TTTAGGGTTTCAA
*
5838776 TTTAAGGTTTCAA
1 TTTAGGGTTTCAA
* * *
5838789 GTTAAGGCTTCAA
1 TTTAGGGTTTCAA
*
5838802 TTTAGGGTTTTAA
1 TTTAGGGTTTCAA
5838815 TTTA
1 TTTA
5838819 AATTTTAAAG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.46
Consensus pattern (13 bp):
TTTAGGGTTTCAA
Found at i:5838840 original size:46 final size:47
Alignment explanation
Indices: 5838776--5838873 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 47
5838766 AGGGTTTTAA
* * *
5838776 TTTAAGGTTTCAAGTTAA-GGCTTCAATTTAGGGTTTTAATTTAA-AT
1 TTTAAAGTTTCAAGTTAAGGGCTTC-ATTTAAGGTTTCAATTTAAGAT
* * *
5838822 TTTAAAGTTTCGATTTAAGGGTTTCATTTAAGGTTTCAATTTAAGAT
1 TTTAAAGTTTCAAGTTAAGGGCTTCATTTAAGGTTTCAATTTAAGAT
5838869 TTTAA
1 TTTAA
5838874 TTTAAGGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 32 0.73
47 12 0.27
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (47 bp):
TTTAAAGTTTCAAGTTAAGGGCTTCATTTAAGGTTTCAATTTAAGAT
Found at i:5838850 original size:13 final size:14
Alignment explanation
Indices: 5838828--5838880 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
5838818 AAATTTTAAA
*
5838828 GTTTCGATTTAAGG
1 GTTTCAATTTAAGG
5838842 GTTTC-ATTTAA-G
1 GTTTCAATTTAAGG
5838854 GTTTCAATTTAA-G
1 GTTTCAATTTAAGG
* *
5838867 ATTTTAATTTAAGG
1 GTTTCAATTTAAGG
5838881 AATTTATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 6 0.17
13 23 0.66
14 6 0.17
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (14 bp):
GTTTCAATTTAAGG
Found at i:5838876 original size:26 final size:26
Alignment explanation
Indices: 5838822--5838880 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
5838812 TAATTTAAAT
* * * *
5838822 TTTAAAGTTTCGATTTAAGGGTTTCA
1 TTTAAGGTTTCAATTTAAGAGTTTAA
*
5838848 TTTAAGGTTTCAATTTAAGATTTTAA
1 TTTAAGGTTTCAATTTAAGAGTTTAA
5838874 TTTAAGG
1 TTTAAGG
5838881 AATTTATGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (26 bp):
TTTAAGGTTTCAATTTAAGAGTTTAA
Found at i:5839222 original size:15 final size:15
Alignment explanation
Indices: 5839204--5839237 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5839194 ATGGCAAGTT
* *
5839204 TAATAACAATAGTAA
1 TAATAAAAATAGCAA
5839219 TAATAAAAATAGCAA
1 TAATAAAAATAGCAA
5839234 TAAT
1 TAAT
5839238 GATGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
TAATAAAAATAGCAA
Found at i:5839873 original size:52 final size:52
Alignment explanation
Indices: 5839790--5839905 Score: 153
Period size: 52 Copynumber: 2.2 Consensus size: 52
5839780 TAATAGGCCA
* *
5839790 ACAATGTAAAGACAAACGATAATATACATGGCAACCAGCGAGCAAAAGGATT
1 ACAAAGTAAAGACAAACGATAATATACATGGCAACCAACGAGCAAAAGGATT
* * *
5839842 ACAAAGTAAAGACCAATC-ATAATATGCATGGCGACCAACGAGCAAAAGGATT
1 ACAAAGTAAAGA-CAAACGATAATATACATGGCAACCAACGAGCAAAAGGATT
* *
5839894 AAAAAGGAAAGA
1 ACAAAGTAAAGA
5839906 TCTTCCTCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 52 0.93
53 4 0.07
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (52 bp):
ACAAAGTAAAGACAAACGATAATATACATGGCAACCAACGAGCAAAAGGATT
Found at i:5842571 original size:23 final size:23
Alignment explanation
Indices: 5842545--5842589 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5842535 TTCACTCAAT
*
5842545 CATTTATTTCTTT-TTTTCTTTTC
1 CATTT-TTTCTTTGATTTCTTTTC
5842568 CATTTTTTCTTTGATTTCTTTT
1 CATTTTTTCTTTGATTTCTTTT
5842590 GTTTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (23 bp):
CATTTTTTCTTTGATTTCTTTTC
Found at i:5842603 original size:7 final size:7
Alignment explanation
Indices: 5842591--5842629 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
5842581 ATTTCTTTTG
5842591 TTTTTCT
1 TTTTTCT
5842598 TTTTTCAT
1 TTTTTC-T
*
5842606 TTCTT-T
1 TTTTTCT
5842612 TTTTTCT
1 TTTTTCT
5842619 TTTTTCT
1 TTTTTCT
5842626 TTTT
1 TTTT
5842630 GTTTCTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.18
7 18 0.64
8 5 0.18
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:5842615 original size:21 final size:23
Alignment explanation
Indices: 5842581--5842624 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
5842571 TTTTTCTTTG
5842581 ATTTCTTTTGTTTTTCTTTTTTC
1 ATTTCTTTTGTTTTTCTTTTTTC
5842604 ATTTC-TTT-TTTTTCTTTTTTC
1 ATTTCTTTTGTTTTTCTTTTTTC
5842625 TTTTTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.62
22 3 0.14
23 5 0.24
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (23 bp):
ATTTCTTTTGTTTTTCTTTTTTC
Found at i:5842622 original size:28 final size:27
Alignment explanation
Indices: 5842550--5842629 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
5842540 TCAATCATTT
*
5842550 ATTTC-TTTTTTTCTTTTCCATTTTTTC
1 ATTTCTTTTTTTTCTTTTTC-TTTTTTC
* * *
5842577 -TTTGATTTCTTTTGTTTTTCTTTTTTC
1 ATTT-CTTTTTTTTCTTTTTCTTTTTTC
5842604 ATTTCTTTTTTTTCTTTTTTCTTTTT
1 ATTTCTTTTTTTTC-TTTTTCTTTTT
5842630 GTTTCTTTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
26 3 0.07
27 14 0.33
28 25 0.60
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.79
Consensus pattern (27 bp):
ATTTCTTTTTTTTCTTTTTCTTTTTTC
Found at i:5842638 original size:21 final size:20
Alignment explanation
Indices: 5842593--5842680 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 20
5842583 TTCTTTTGTT
5842593 TTTCTTTTTTCATTTCTTTTT-
1 TTTCTTTTTTC-TTT-TTTTTC
5842614 TTTCTTTTTTCTTTTTGTTTC
1 TTTCTTTTTTCTTTTT-TTTC
* * *
5842635 TTTCCTTTTCCTTATTTTTC
1 TTTCTTTTTTCTTTTTTTTC
* ***
5842655 ATTCTTTCACCTTTTCTTTTC
1 TTTCTTTTTTCTTTT-TTTTC
5842676 TTTCT
1 TTTCT
5842681 CTTTGAGTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
19 2 0.04
20 20 0.36
21 33 0.60
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTTTTC
Found at i:5843166 original size:13 final size:13
Alignment explanation
Indices: 5843148--5843185 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5843138 TTACTTTGTC
5843148 TTCATTTTTTTAT
1 TTCATTTTTTTAT
5843161 TTCATTTCTTTT-T
1 TTCATTT-TTTTAT
*
5843174 TTCTTTTTTTTA
1 TTCATTTTTTTA
5843186 AGCAAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCATTTTTTTAT
Found at i:5854442 original size:19 final size:19
Alignment explanation
Indices: 5854418--5854456 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5854408 GCTCTAAAAT
5854418 ATTGAAAAAATTTTGAAGA
1 ATTGAAAAAATTTTGAAGA
* **
5854437 ATTGAAGAGGTTTTGAAGA
1 ATTGAAAAAATTTTGAAGA
5854456 A
1 A
5854457 CTCGAAGAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (19 bp):
ATTGAAAAAATTTTGAAGA
Found at i:5854465 original size:20 final size:19
Alignment explanation
Indices: 5854428--5854465 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5854418 ATTGAAAAAA
*
5854428 TTTTGAAGAATTGAAGAGG
1 TTTTGAAGAATCGAAGAGG
5854447 TTTTGAAGAACTCGAAGAG
1 TTTTGAAGAA-TCGAAGAG
5854466 CAAAGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (19 bp):
TTTTGAAGAATCGAAGAGG
Found at i:5859030 original size:21 final size:21
Alignment explanation
Indices: 5858987--5859042 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
5858977 TTAGCAAAAG
*
5858987 CTTTTAATAAAAACTGTGCAAT
1 CTTTTAA-AAAAAGTGTGCAAT
5859009 CTTTTAAAAAAAGTG-GCTAAT
1 CTTTTAAAAAAAGTGTGC-AAT
* *
5859030 CGTTTGAAAAAAG
1 CTTTTAAAAAAAG
5859043 ATTGGCATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.07
21 21 0.70
22 7 0.23
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (21 bp):
CTTTTAAAAAAAGTGTGCAAT
Found at i:5859757 original size:33 final size:33
Alignment explanation
Indices: 5859715--5859779 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5859705 AATTAGGACA
*
5859715 TAAAAAAAAAAAAACCTGCTAAGTTGAAAATCT
1 TAAAAAAAAAAAAACCTACTAAGTTGAAAATCT
* *
5859748 TAAAAAAAAAAAAGCCTACTAAGTTTAAAATC
1 TAAAAAAAAAAAAACCTACTAAGTTGAAAATC
5859780 CTACAAAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.22
Consensus pattern (33 bp):
TAAAAAAAAAAAAACCTACTAAGTTGAAAATCT
Found at i:5861041 original size:84 final size:84
Alignment explanation
Indices: 5860900--5861064 Score: 321
Period size: 84 Copynumber: 2.0 Consensus size: 84
5860890 CAAAAAACAC
5860900 AATTTTCTACTTGAGATGCAAGTTTACAAAATTCATGTTGATTAGAAATTGAAGCTTCACTATTA
1 AATTTTCTACTTGAGATGCAAGTTTACAAAATTCATGTTGATTAGAAATTGAAGCTTCACTATTA
5860965 GCATGAGATGTTCACTCAT
66 GCATGAGATGTTCACTCAT
*
5860984 AATTTTCTACTTGAGATGCAAGTTTACGAAATTCATGTTGATTAGAAATTGAAGCTTCACTATTA
1 AATTTTCTACTTGAGATGCAAGTTTACAAAATTCATGTTGATTAGAAATTGAAGCTTCACTATTA
5861049 GCATGAGATGTTCACT
66 GCATGAGATGTTCACT
5861065 TTGGTTTGAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (84 bp):
AATTTTCTACTTGAGATGCAAGTTTACAAAATTCATGTTGATTAGAAATTGAAGCTTCACTATTA
GCATGAGATGTTCACTCAT
Found at i:5863657 original size:23 final size:25
Alignment explanation
Indices: 5863630--5863686 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
5863620 AAAATATATA
5863630 TTTAAT-AT-GCATGGTATTAATTC
1 TTTAATGATAGCATGGTATTAATTC
* *
5863653 TTTAATGATAAGCATGGTGTTGATTC
1 TTTAATGAT-AGCATGGTATTAATTC
*
5863679 TTTGATGA
1 TTTAATGA
5863687 AAAGAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 2 0.07
26 20 0.71
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (25 bp):
TTTAATGATAGCATGGTATTAATTC
Found at i:5864574 original size:20 final size:21
Alignment explanation
Indices: 5864541--5864590 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5864531 GATTAATTAT
*
5864541 ATTATTTAATTTAATCATATA
1 ATTAATTAATTTAATCATATA
**
5864562 ATTAATTAA-TTAATTTTATA
1 ATTAATTAATTTAATCATATA
5864582 ATTAATTAA
1 ATTAATTAA
5864591 ACATGTCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAATTAATTTAATCATATA
Found at i:5865043 original size:32 final size:32
Alignment explanation
Indices: 5864955--5865047 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
5864945 ATCTCGTTTG
* * *
5864955 TTCAAGATCAAGTCAACAA-GACCCTTTAAGCA
1 TTCAAGAACAAGTC-TCAACGACCCTTGAAGCA
*
5864987 TTCAAGAACAAGTCTCAACAACCCTTGAAGCA
1 TTCAAGAACAAGTCTCAACGACCCTTGAAGCA
* *
5865019 TTTAAGAACAAGTCT-ACCTGACCCTTGAA
1 TTCAAGAACAAGTCTCAAC-GACCCTTGAA
5865048 ATGGATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.10
32 47 0.90
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (32 bp):
TTCAAGAACAAGTCTCAACGACCCTTGAAGCA
Found at i:5867880 original size:21 final size:21
Alignment explanation
Indices: 5867854--5867933 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
5867844 AATTCTCATG
5867854 AAACCCTAAACCCTAAATCTT
1 AAACCCTAAACCCTAAATCTT
* * *
5867875 AAACCCCAAA-CTTGAAACCTT
1 AAACCCTAAACCCT-AAATCTT
* *
5867896 AGACCCTAAGCCCTAAATCTT
1 AAACCCTAAACCCTAAATCTT
* **
5867917 AAGCTATAAACCCTAAA
1 AAACCCTAAACCCTAAA
5867934 CCTAAAAAAC
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.42, C:0.31, G:0.05, T:0.21
Consensus pattern (21 bp):
AAACCCTAAACCCTAAATCTT
Found at i:5869589 original size:21 final size:20
Alignment explanation
Indices: 5869550--5869589 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5869540 TTTAGACATC
*
5869550 TTTGCATTTCATGACATTCT
1 TTTGCATTTCATCACATTCT
*
5869570 TTTGCATTATCATCATATTC
1 TTTGCATT-TCATCACATTC
5869590 GTACATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTGCATTTCATCACATTCT
Found at i:5873261 original size:9 final size:8
Alignment explanation
Indices: 5873232--5873355 Score: 60
Period size: 9 Copynumber: 14.9 Consensus size: 8
5873222 AAGGAAGGAA
5873232 AAAATAAAG
1 AAAA-AAAG
5873241 AAAATAAAG
1 AAAA-AAAG
5873250 AAAAAAATG
1 AAAAAAA-G
5873259 AAAGAAAA-
1 AAA-AAAAG
5873267 AATAAAAAG
1 AA-AAAAAG
5873276 AGAGAAAAAG
1 A-A-AAAAAG
*
5873286 AAAGAAA-
1 AAAAAAAG
*
5873293 ATAAAAAG
1 AAAAAAAG
* *
5873301 GAAAAATG
1 AAAAAAAG
5873309 --AAAAA-
1 AAAAAAAG
*
5873314 AAAAAGAG
1 AAAAAAAG
5873322 AAAAGAAAG
1 AAAA-AAAG
**
5873331 AAAAAGGG
1 AAAAAAAG
5873339 AAAAAAGAAG
1 -AAAAA-AAG
5873349 AAAAAAA
1 AAAAAAA
5873356 ATGAATGATT
Statistics
Matches: 89, Mismatches: 14, Indels: 25
0.70 0.11 0.20
Matches are distributed among these distances:
6 4 0.04
7 9 0.10
8 26 0.29
9 37 0.42
10 13 0.15
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5873264 original size:13 final size:13
Alignment explanation
Indices: 5873241--5873318 Score: 53
Period size: 12 Copynumber: 6.3 Consensus size: 13
5873231 AAAAATAAAG
5873241 AAAAT-AAAGAAA
1 AAAATGAAAGAAA
5873253 AAAATGAAAG-AA
1 AAAATGAAAGAAA
*
5873265 AAAATAAAAAGAGAGA
1 AAAAT-GAAAGA-A-A
5873281 AAAA-GAAAGAAA
1 AAAATGAAAGAAA
* *
5873293 ATAA--AAAG-GA
1 AAAATGAAAGAAA
5873303 AAAATGAAA-AAA
1 AAAATGAAAGAAA
5873315 AAAA
1 AAAA
5873319 GAGAAAAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
10 4 0.08
11 4 0.08
12 24 0.46
13 9 0.17
14 5 0.10
15 1 0.02
16 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAATGAAAGAAA
Found at i:5873294 original size:49 final size:50
Alignment explanation
Indices: 5873231--5873336 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 50
5873221 GAAGGAAGGA
* * * *
5873231 AAAAATAAAGAAAATAAAGAA-AAAAATGAAAGAAAAAATA-AAAAGAGAG
1 AAAAAGAAAGAAAATAAA-AAGAAAAATGAAAAAAAAAAGAGAAAAGAAAG
5873280 AAAAAGAAAGAAAATAAAAAGGAAAAATGAAAAAAAAAAGAGAAAAGAAAG
1 AAAAAGAAAGAAAATAAAAA-GAAAAATGAAAAAAAAAAGAGAAAAGAAAG
5873331 AAAAAG
1 AAAAAG
5873337 GGAAAAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
48 2 0.04
49 17 0.34
50 17 0.34
51 14 0.28
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (50 bp):
AAAAAGAAAGAAAATAAAAAGAAAAATGAAAAAAAAAAGAGAAAAGAAAG
Found at i:5873347 original size:15 final size:16
Alignment explanation
Indices: 5873259--5873344 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 16
5873249 GAAAAAAATG
*
5873259 AAAGAAAAA-ATAAAA
1 AAAGAAAAAGAGAAAA
*
5873274 AGAGAGAAAAAGA-AAGA
1 A-A-AGAAAAAGAGAAAA
* *
5873291 AAATAAAAAGGAAAAATGA
1 AAAGAAAAA-GAGAAA--A
*
5873310 AAAAAAAAAGAGAAAA
1 AAAGAAAAAGAGAAAA
*
5873326 GAAAGAAAAAGGGAAAA
1 -AAAGAAAAAGAGAAAA
5873343 AA
1 AA
5873345 GAAGAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
15 7 0.12
16 7 0.12
17 27 0.48
18 6 0.11
19 9 0.16
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAGAGAAAA
Found at i:5873354 original size:10 final size:10
Alignment explanation
Indices: 5873270--5873354 Score: 54
Period size: 10 Copynumber: 8.5 Consensus size: 10
5873260 AAGAAAAAAT
5873270 AAAAAG-AGA
1 AAAAAGAAGA
5873279 GAAAAAGAAAGA
1 -AAAAAG-AAGA
*
5873291 AAATAAAAAGGA
1 AAA-AAGAA-GA
*
5873303 AAAATGAA-A
1 AAAAAGAAGA
5873312 AAAAA-AAGA
1 AAAAAGAAGA
*
5873321 GAAAAGAA-A
1 AAAAAGAAGA
*
5873330 GAAAAAG-GGA
1 -AAAAAGAAGA
5873340 AAAAAGAAGA
1 AAAAAGAAGA
5873350 AAAAA
1 AAAAA
5873355 AATGAATGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
8 2 0.03
9 17 0.29
10 21 0.36
11 8 0.14
12 10 0.17
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:5873356 original size:50 final size:48
Alignment explanation
Indices: 5873231--5873360 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 48
5873221 GAAGGAAGGA
* * * * *
5873231 AAAAATAAAGAAAATAAAGAAAAAAATGAAAGAAAAAATAAAAAGAGAG
1 AAAAAGAAAGAAAAGAAA-AAAAAAATGAAAAAAAAAAGAAAAAGAAAG
*
5873280 AAAAAGAAAGAAAATAAAAAGGAAAAATGAAAAAAAAAAGAGAAAAGAAAG
1 AAAAAGAAAGAAAAGAAAAA--AAAAATGAAAAAAAAAAGA-AAAAGAAAG
*
5873331 AAAAAGGGAA-AAAAGAAGAAAAAAAATGAA
1 AAAAA-GAAAGAAAAGAA-AAAAAAAATGAA
5873361 TGATTGAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
48 2 0.03
49 17 0.24
50 26 0.37
51 19 0.27
52 6 0.09
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (48 bp):
AAAAAGAAAGAAAAGAAAAAAAAAATGAAAAAAAAAAGAAAAAGAAAG
Found at i:5874799 original size:13 final size:12
Alignment explanation
Indices: 5874771--5874810 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5874761 TCCAAAAACC
*
5874771 AAAACAAAAGAA
1 AAAAAAAAAGAA
*
5874783 AAAAGAAAAGAA
1 AAAAAAAAAGAA
5874795 AAAAAAAGAAGAA
1 AAAAAAA-AAGAA
5874808 AAA
1 AAA
5874811 TTGAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:5875080 original size:32 final size:30
Alignment explanation
Indices: 5875044--5875154 Score: 81
Period size: 32 Copynumber: 3.7 Consensus size: 30
5875034 TGATATTTAA
5875044 GTTTTCTTCAATGGTGATATTCAAAGTCATTT
1 GTTTTCTT-AATGGTGATATTCAAAGTC-TTT
** **
5875076 GTTTTCACTCGATGGTGATA-TCTGAGTC--T
1 GTTTT--CTTAATGGTGATATTCAAAGTCTTT
5875105 -TTTT-TT-ATGGTGATATTCAAAGTCTTTT
1 GTTTTCTTAATGGTGATATTCAAAGTC-TTT
*
5875133 ATTTTACTTAATGGTGATATTC
1 GTTTT-CTTAATGGTGATATTC
5875155 GAGTCCTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
24 9 0.15
25 7 0.11
28 5 0.08
29 5 0.08
31 2 0.03
32 23 0.37
33 9 0.15
34 2 0.03
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.49
Consensus pattern (30 bp):
GTTTTCTTAATGGTGATATTCAAAGTCTTT
Found at i:5875115 original size:57 final size:56
Alignment explanation
Indices: 5875054--5875493 Score: 381
Period size: 57 Copynumber: 7.8 Consensus size: 56
5875044 GTTTTCTTCA
* * * * *
5875054 ATGGTGATATTCAAAGTCATTTGTTTTCACTCGATGGTGATATCTGAGTCTTTTTTT
1 ATGGTGATATTCAAAGTCTTTTGTTTT-ACTCAATGGTGATATCCGAGTCCTTTTTG
* * * *
5875111 ATGGTGATATTCAAAGTCTTTTATTTTACTTAATGGTGATATTCGAGTCC-TTTTC
1 ATGGTGATATTCAAAGTCTTTTGTTTTACTCAATGGTGATATCCGAGTCCTTTTTG
* *
5875166 AGTAGTGATATTCAAAGTCTTTTATTTTACTCAATGGTGATATCCGAGT-CTTTTTCG
1 A-TGGTGATATTCAAAGTCTTTTGTTTTACTCAATGGTGATATCCGAGTCCTTTTT-G
* * * *
5875223 ATGGTGATATCCAAAGGT-TTTTGTATTTACTCAGTGGTAATATCCAAGTCCCTTTTT-
1 ATGGTGATATTCAAA-GTCTTTTGT-TTTACTCAATGGTGATATCCGAGT-CCTTTTTG
* * * **
5875280 ATGGTGATATCCAAAGT-TATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCA
1 ATGGTGATATTCAAAGTCT-TTTGTTTT-ACTCAATGGTGATATCCGAGTCCTTTTTG
** * * * *
5875337 ATGGTGATATTTGAAGTCTTTTATTTTATTC-ATGGTGATATCCCAGTCCTCTTTG
1 ATGGTGATATTCAAAGTCTTTTGTTTTACTCAATGGTGATATCCGAGTCCTTTTTG
* * * ** *
5875392 CTGGTGATATTCGAAGTTTTTTGTTTTTACTTGATGGTGATATCCGAGTTCC-CTTTG
1 ATGGTGATATTCAAAGTCTTTTG-TTTTACTCAATGGTGATATCCGAG-TCCTTTTTG
* ** * * **
5875449 ATAGTGATATTTGAAGTCATTTGTTTTCATTCGGTGGTGATATCC
1 ATGGTGATATTCAAAGTCTTTTGTTTT-ACTCAATGGTGATATCC
5875494 AAGTTCCCTT
Statistics
Matches: 321, Mismatches: 47, Indels: 30
0.81 0.12 0.08
Matches are distributed among these distances:
55 44 0.14
56 108 0.34
57 159 0.50
58 4 0.01
59 6 0.02
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (56 bp):
ATGGTGATATTCAAAGTCTTTTGTTTTACTCAATGGTGATATCCGAGTCCTTTTTG
Found at i:5875227 original size:112 final size:112
Alignment explanation
Indices: 5875055--5875440 Score: 406
Period size: 112 Copynumber: 3.4 Consensus size: 112
5875045 TTTTCTTCAA
* * * **
5875055 TGGTGATATTCAAAGTCATTTGTTTTCACTCGATGGTGATATCTGAGTCTTTTTTTATGGTGATA
1 TGGTGATATTCAAAGTCTTTTGTTTTCACTCAATGGTGATATCCGAGTCTTTTTCAATGGTGATA
* *
5875120 TTCAAAGTCTTTTATTTTACTTAATGGTGATATTCGAGTCCTTTTCAG
66 TTCAAAGTCTTTTATTTTACTTAATGGTGATATCCAAGTCCTTTT-AG
* * *
5875168 TAGTGATATTCAAAGTCTTTTATTTT-ACTCAATGGTGATATCCGAGTCTTTTTCGATGGTGATA
1 TGGTGATATTCAAAGTCTTTTGTTTTCACTCAATGGTGATATCCGAGTCTTTTTCAATGGTGATA
* * * * *
5875232 TCCAAAGGT-TTTTGTATTTACTCAGTGGTAATATCCAAGTCCCTTTTTA-
66 TTCAAA-GTCTTTTAT-TTTACTTAATGGTGATATCCAAGT-CC-TTTTAG
* * * *
5875281 TGGTGATATCCAAAGT-TATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCAATGGTGAT
1 TGGTGATATTCAAAGTCT-TTTGTTTTCACTCAATGGTGATATCCGAGTCTTTTTCAATGGTGAT
** * *
5875345 ATTTGAAGTCTTTTATTTTA-TTCATGGTGATATCCCAGTCCTCTTT-G
65 ATTCAAAGTCTTTTATTTTACTTAATGGTGATATCCAAGTCCT-TTTAG
* * * **
5875392 CTGGTGATATTCGAAGTTTTTTGTTTTTACTTGATGGTGATATCCGAGT
1 -TGGTGATATTCAAAGTCTTTTGTTTTCACTCAATGGTGATATCCGAGT
5875441 TCCCTTTGAT
Statistics
Matches: 225, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
110 1 0.00
111 5 0.02
112 98 0.44
113 72 0.32
114 45 0.20
115 4 0.02
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (112 bp):
TGGTGATATTCAAAGTCTTTTGTTTTCACTCAATGGTGATATCCGAGTCTTTTTCAATGGTGATA
TTCAAAGTCTTTTATTTTACTTAATGGTGATATCCAAGTCCTTTTAG
Found at i:5875489 original size:169 final size:170
Alignment explanation
Indices: 5875114--5875497 Score: 436
Period size: 169 Copynumber: 2.3 Consensus size: 170
5875104 TTTTTTTATG
* * * * * *
5875114 GTGATATTCAAAGTCTTTTATTTT-ACTTAATGGTGATATTCGAGTCCTTTTCAGTAGTGATATT
1 GTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCAATAGTGATATT
* *
5875178 CAAAGTCTTTTATTTTACTCAATGGTGATATCCGAGTCTTTTTCGATGGTGATATCCAAAGGTTT
66 CAAAGTCTTTTATTTTACTCAATGGTGATATCCCAGTCTCTTTCGATGGTGATATCCAAAGGTTT
* *
5875243 TTGTATTTACTCAGTGGTAATATCCAAGTCCCTTTTTATG
131 TTGTATTTACTCAGTGGTAATATCCAAGTCCCTTTTGATA
* *
5875283 GTGATATCCAAAGTTATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCAATGGTGATATT
1 GTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCAATAGTGATATT
** * * * * *
5875348 TGAAGTCTTTTATTTTATTC-ATGGTGATATCCCAGTCCTCTTT-GCTGGTGATATTCGAAGTTT
66 CAAAGTCTTTTATTTTACTCAATGGTGATATCCCAGT-CTCTTTCGATGGTGATATCCAAAGGTT
* * * *
5875411 TTTGTTTTTACT-TGATGGTGATATCCGAGTTCCC-TTTGATA
130 TTTGTATTTACTCAG-TGGTAATATCCAAG-TCCCTTTTGATA
*** * ** *
5875452 GTGATATTTGAAGTCATTTGTTTTCATTCGGTGGTGATATCCAAGT
1 GTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATTCAAGT
5875498 TCCCTTTGAT
Statistics
Matches: 180, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
168 1 0.01
169 117 0.65
170 62 0.34
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (170 bp):
GTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCAATAGTGATATT
CAAAGTCTTTTATTTTACTCAATGGTGATATCCCAGTCTCTTTCGATGGTGATATCCAAAGGTTT
TTGTATTTACTCAGTGGTAATATCCAAGTCCCTTTTGATA
Found at i:5875494 original size:226 final size:226
Alignment explanation
Indices: 5875054--5875504 Score: 529
Period size: 226 Copynumber: 2.0 Consensus size: 226
5875044 GTTTTCTTCA
* * * * **
5875054 ATGGTGATATTCAAAGTCATTTGTTTTCACTCGATGGTGATATCTGAGTCTTTTTTTATGGTGAT
1 ATGGTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATCTAAGTCCTTTTCAATGGTGAT
* *
5875119 ATTCAAAGTCTTTTATTTTACTTAATGGTGATATTCGAGTCCTTTTCAGTAGTGATATTCAAAGT
66 ATTCAAAGTCTTTTATTTTACTTAATGGTGATATCCCAGTCCTTTTCA-TAGTGATATTCAAAGT
** * *
5875184 CTTTTATTTTACTCAATGGTGATATCCGAGTCTTTTTCGATGGTGATATCCAAAGGTTTTTGTAT
130 CTTTTATTTTACTCAATGGTGATATCCGAGTCCCTTTCGATAGTGATATCCAAAGGTATTTGTAT
5875249 TTACTCAGTGGTAATATCCAAG-TCCCTTTTT
195 TTACTCAGTGGTAATATCCAAGTTCCCTTTTT
*
5875280 ATGGTGATATCCAAAGTTATTTGTTTTCACTCAATGGTGATAT-TCAAGTCCTTTTCAATGGTGA
1 ATGGTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATCT-AAGTCCTTTTCAATGGTGA
** * * *
5875344 TATTTGAAGTCTTTTATTTTA-TTCATGGTGATATCCCAGTCCTCTTTGC-TGGTGATATTCGAA
65 TATTCAAAGTCTTTTATTTTACTTAATGGTGATATCCCAGTCCT-TTT-CATAGTGATATTCAAA
* * ** ***
5875407 GTTTTTTGTTTTTACTTGATGGTGATATCCGAGTTCCCTTT-GATAGTGATATTTGAA-GTCATT
128 GTCTTTT-ATTTTACTCAATGGTGATATCCGAG-TCCCTTTCGATAGTGATATCCAAAGGT-ATT
* * *
5875470 TGT-TTTCATTCGGTGGTGATATCCAAGTTCCCTTT
190 TGTATTT-ACTCAGTGGTAATATCCAAGTTCCCTTT
5875505 GATATTTGAC
Statistics
Matches: 189, Mismatches: 28, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
225 43 0.23
226 133 0.70
227 13 0.07
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (226 bp):
ATGGTGATATCCAAAGTCATTTGTTTTCACTCAATGGTGATATCTAAGTCCTTTTCAATGGTGAT
ATTCAAAGTCTTTTATTTTACTTAATGGTGATATCCCAGTCCTTTTCATAGTGATATTCAAAGTC
TTTTATTTTACTCAATGGTGATATCCGAGTCCCTTTCGATAGTGATATCCAAAGGTATTTGTATT
TACTCAGTGGTAATATCCAAGTTCCCTTTTT
Found at i:5875499 original size:57 final size:56
Alignment explanation
Indices: 5875054--5875578 Score: 306
Period size: 57 Copynumber: 9.4 Consensus size: 56
5875044 GTTTTCTTCA
* * ** ** *
5875054 ATGGTGATATTCAAAGTCATTTGTTTTCACTCGATGGTGATATCTGAGTCTTTTTTT
1 ATGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAGTC-CCTTTG
* * * * * * * *
5875111 ATGGTGATATTCAAAGTCTTTTATTTT-ACTT-AATGGTGATATTCGAGTCCTTTTC
1 ATGGTGATATTCGAAGTCATTTGTTTTCA-TTCGATGGTGATATCCAAGTCCCTTTG
* * * * * * * **
5875166 AGTAGTGATATTCAAAGTCTTTTATTTT-ACTCAATGGTGATATCCGAGTCTTTTTCG
1 A-TGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAGTCCCTTT-G
* * * * * *
5875223 ATGGTGATATCCAAAGGT-TTTTGTATTT-ACTC-AGTGGTAATATCCAAGTCCCTTTTT
1 ATGGTGATATTCGAA-GTCATTTGT-TTTCATTCGA-TGGTGATATCCAAGTCCC-TTTG
* * * * * * * *
5875280 ATGGTGATATCCAAAGTTATTTGTTTTCACTCAATGGTGATATTCAAGTCCTTTTCA
1 ATGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAGTCCCTTT-G
* * * *
5875337 ATGGTGATATTTGAAGTCTTTTATTTT-ATTC-ATGGTGATATCCCAGTCCTCTTTG
1 ATGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAGTCC-CTTTG
* ** * *
5875392 CTGGTGATATTCGAAGTTTTTTGTTTTTACTT-GATGGTGATATCCGAGTTCCCTTTG
1 ATGGTGATATTCGAAGTCATTTGTTTTCA-TTCGATGGTGATATCCAAG-TCCCTTTG
* * *
5875449 ATAGTGATATTTGAAGTCATTTGTTTTCATTCGGTGGTGATATCCAAGTTCCCTTTG
1 ATGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAG-TCCCTTTG
* * * * *
5875506 A---T-AT-TT-GACGCCGTTTGTTTTCATTTGATGGTGATATCCGAGTTCCCTTTG
1 ATGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAG-TCCCTTTG
* *
5875557 ATGGCGATATCCGAAGTCATTT
1 ATGGTGATATTCGAAGTCATTT
5875579 ACATTTGCTT
Statistics
Matches: 383, Mismatches: 61, Indels: 48
0.78 0.12 0.10
Matches are distributed among these distances:
51 40 0.10
52 2 0.01
53 2 0.01
54 1 0.00
55 47 0.12
56 99 0.26
57 185 0.48
58 7 0.02
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.45
Consensus pattern (56 bp):
ATGGTGATATTCGAAGTCATTTGTTTTCATTCGATGGTGATATCCAAGTCCCTTTG
Found at i:5875529 original size:51 final size:51
Alignment explanation
Indices: 5875453--5875558 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
5875443 CCTTTGATAG
* *
5875453 TGATATTTGAAGTCATTTGTTTTCATTCGGTGGTGATATCCAAGTTCCCTT
1 TGATATTTGAAGCCATTTGTTTTCATTCGATGGTGATATCCAAGTTCCCTT
* * * *
5875504 TGATATTTGACGCCGTTTGTTTTCATTTGATGGTGATATCCGAGTTCCCTT
1 TGATATTTGAAGCCATTTGTTTTCATTCGATGGTGATATCCAAGTTCCCTT
5875555 TGAT
1 TGAT
5875559 GGCGATATCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (51 bp):
TGATATTTGAAGCCATTTGTTTTCATTCGATGGTGATATCCAAGTTCCCTT
Found at i:5876729 original size:29 final size:29
Alignment explanation
Indices: 5876671--5876741 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5876661 GTGTTAGTCA
* *
5876671 TGTCTATTCGTGTATATCCATGTTAGTTG
1 TGTCTATTCGTATATATCCATATTAGTTG
* *
5876700 TGTCTATTCGTATATATTCATATTATTTG
1 TGTCTATTCGTATATATCCATATTAGTTG
*
5876729 TGTTTATTCGTAT
1 TGTCTATTCGTAT
5876742 CATGTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (29 bp):
TGTCTATTCGTATATATCCATATTAGTTG
Found at i:5878351 original size:22 final size:23
Alignment explanation
Indices: 5878325--5878367 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5878315 TAAATTTAAA
5878325 ATAATAT-TTTATATTT-TTAATT
1 ATAATATATTT-TATTTGTTAATT
5878347 ATAATATATTTTATTTGTTAA
1 ATAATATATTTTATTTGTTAA
5878368 ATATTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATAATATATTTTATTTGTTAATT
Found at i:5878478 original size:32 final size:32
Alignment explanation
Indices: 5878442--5878510 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
5878432 ATCCTTTTAA
* * *
5878442 AAAAAT-TCCATTTCATTTTTAAAAAATTACAT
1 AAAAATATCCATATCA-ATTTAAAAAATTAAAT
**
5878474 AAAAATATTTATATCAATTTAAAAAATTAAAT
1 AAAAATATCCATATCAATTTAAAAAATTAAAT
5878506 AAAAA
1 AAAAA
5878511 ACTTCATAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (32 bp):
AAAAATATCCATATCAATTTAAAAAATTAAAT
Found at i:5880293 original size:11 final size:11
Alignment explanation
Indices: 5880277--5880310 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5880267 AATGAATAGG
5880277 AAAATATTATA
1 AAAATATTATA
*
5880288 AAAATAATTTTA
1 AAAAT-ATTATA
5880300 AAAATATTATA
1 AAAATATTATA
5880311 TTATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATTATA
Found at i:5880529 original size:19 final size:20
Alignment explanation
Indices: 5880487--5880529 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5880477 TGTATGCAAA
* *
5880487 ATTAATATATTTTTATTGTT
1 ATTAAAATATTTATATTGTT
5880507 -TTAAAATATTTATATT-TT
1 ATTAAAATATTTATATTGTT
5880525 ATTAA
1 ATTAA
5880530 TTACTAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTAAAATATTTATATTGTT
Found at i:5881185 original size:15 final size:14
Alignment explanation
Indices: 5881167--5881217 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 14
5881157 TTTATTTATT
5881167 TACAAAATATTGTCA
1 TACAAAATATT-TCA
5881182 TACAAAA-ATTTCA
1 TACAAAATATTTCA
*
5881195 TA-AAAA-ATATCA
1 TACAAAATATTTCA
5881207 TTACAAAATAT
1 -TACAAAATAT
5881218 CATGCAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 9 0.28
13 7 0.22
14 7 0.22
15 9 0.28
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (14 bp):
TACAAAATATTTCA
Found at i:5881202 original size:12 final size:13
Alignment explanation
Indices: 5881179--5881244 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 13
5881169 CAAAATATTG
*
5881179 TCATACAAAAATT
1 TCATACAAAAATA
5881192 TCATA-AAAAATA
1 TCATACAAAAATA
5881204 TCATTAC-AAAATA
1 TCA-TACAAAAATA
* *
5881217 TCATGC-AAAACA
1 TCATACAAAAATA
*
5881229 TCATA-ATAAATA
1 TCATACAAAAATA
5881241 TCAT
1 TCAT
5881245 GCCAATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
12 28 0.64
13 16 0.36
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.29
Consensus pattern (13 bp):
TCATACAAAAATA
Found at i:5883322 original size:42 final size:43
Alignment explanation
Indices: 5883190--5883336 Score: 158
Period size: 43 Copynumber: 3.4 Consensus size: 43
5883180 AAGGGTTCGA
* *
5883190 AACTTTTGAAAAAT-AAATGCTCCCCCCTTAACAGAAG-CTTTGG
1 AACTTTTGAAAAATAAAATGCT-CCCCCTCAATA-AAGACTTTGG
** * *
5883233 AACTTTTGAAAAATAAAATGCTCCTTCTCAATAAAGGCTTTGA
1 AACTTTTGAAAAATAAAATGCTCCCCCTCAATAAAGACTTTGG
** *
5883276 AACTTTCAAAAAATAAAATGC-CCCCCTCATTTAAA-ACTTTGG
1 AACTTTTGAAAAATAAAATGCTCCCCCTCA-ATAAAGACTTTGG
5883318 AACTTTTGAAAAATAAAAT
1 AACTTTTGAAAAATAAAAT
5883337 AGATATCTGG
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 31 0.36
43 49 0.56
44 7 0.08
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (43 bp):
AACTTTTGAAAAATAAAATGCTCCCCCTCAATAAAGACTTTGG
Found at i:5893581 original size:144 final size:143
Alignment explanation
Indices: 5893337--5893879 Score: 433
Period size: 145 Copynumber: 3.7 Consensus size: 143
5893327 GAAAAAGGTC
*
5893337 AAATTACCAAAATACCTTTATAAGGGGGTATTTTCA-TAATTTGACCTTTCTGAGCTC-GAATTT
1 AAATTACCAAAATACCTTTATAA-GGGGTAGTTT-AGTAATTTGACCTTTC-GAGCTCAGAATTT
* * * * * *
5893400 TCTTGAAACCTTCCAGACCTTATTCTTATAATATTTCATGATTTTTTATACATTTAAAATCACAA
63 T-ATGAAACTTTTCAGATC-TATTTTTATAATATTTCATGATTTTTTATACATTTAAAATCATAA
* *
5893465 CGGTCCCCTGAGAAGTGTG
126 CAGT-ACCTGAGAAGTGTG
* *
5893484 AAATTACCAAAATATCTTTAT-AGGGGTA-TTTAGTAA-TTGAATCTTCTCGAGCTCAGAATTTT
1 AAATTACCAAAATACCTTTATAAGGGGTAGTTTAGTAATTTG-ACCTT-TCGAGCTCAGAATTTT
* * ** * *
5893546 ATGAAACTTTTCATATCTCATTTTTGTAATATTTCATGATTTTTGGTGA-GTTTAGAATCATAGT
64 ATGAAACTTTTCAGATCT-ATTTTTATAATATTTCATGATTTTTTAT-ACATTTAAAATCATA--
*** * * *
5893610 ATTTTTCC-AAAAAGTGTG
125 ACAGTACCTGAGAAGTGTG
* * * * * * *
5893628 AAATTACCAAAATACCTTT-TGAGGGGTAGTTTCGTAATTTGGCCTTTTTGATCTCAAAATTTCA
1 AAATTACCAAAATACCTTTATAAGGGGTAGTTTAGTAATTTGACC-TTTCGAGCTCAGAATTTTA
* * * *
5893692 TGAAACTTTTCAGATACTAGTTTTATAATATTTCATGATTTTTTATGCATTTGAAATTATAACAG
65 TGAAACTTTTCAGAT-CTATTTTTATAATATTTCATGATTTTTTATACATTTAAAATCATAACAG
5893757 TACCTCGAGAAGTGT-
129 TACCT-GAGAAGTGTG
* * * *
5893772 AAATTTACCAAAATACCCTTATAA-GGGTATTTTCGTAATTT-AGCCTTTTCGAGCTCAAAATTT
1 AAA-TTACCAAAATACCTTTATAAGGGGTAGTTTAGTAATTTGA-CC-TTTCGAGCTCAGAATTT
* ** * * **
5893835 CACAAAATTTTTCAGATCATAATCCTATAATATTTCATGATTTTT
63 TATGAAACTTTTCAGATC-TATTTTTATAATATTTCATGATTTTT
5893880 GGTATTTTAA
Statistics
Matches: 320, Mismatches: 56, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
143 10 0.03
144 99 0.31
145 179 0.56
146 12 0.04
147 20 0.06
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (143 bp):
AAATTACCAAAATACCTTTATAAGGGGTAGTTTAGTAATTTGACCTTTCGAGCTCAGAATTTTAT
GAAACTTTTCAGATCTATTTTTATAATATTTCATGATTTTTTATACATTTAAAATCATAACAGTA
CCTGAGAAGTGTG
Found at i:5897830 original size:17 final size:17
Alignment explanation
Indices: 5897808--5897855 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
5897798 ATAGATAGCA
* *
5897808 GGCAGCAGTGGGTAGTG
1 GGCAGCAGTGAGCAGTG
5897825 GGCAGCAGTGAGCAGTG
1 GGCAGCAGTGAGCAGTG
5897842 GGCAGCAGTGAGCA
1 GGCAGCAGTGAGCA
5897856 AAAGGCAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.23, C:0.17, G:0.48, T:0.12
Consensus pattern (17 bp):
GGCAGCAGTGAGCAGTG
Found at i:5898950 original size:183 final size:180
Alignment explanation
Indices: 5898643--5898995 Score: 598
Period size: 183 Copynumber: 1.9 Consensus size: 180
5898633 GTTTAGATTT
* *
5898643 AGGTTGCATCATGTTTTTGTATTCATCAAACAACTCAATTATGCTTCTTGCACTTTTTTAATCAT
1 AGGTTGCATCATGTTTTTGTATTCATCAAACAACTCAACTATGCTTCTTGCACTTTCTTAATCAT
*
5898708 CACTGAAGTTTCATCACGAGAATGCATTTTCATAAAGCAAAACTCCACAAATGCAATTTTTTTTT
66 CACTGAAGTTTCATCACGAGAATACATTTTCATAAAGCAAAACTCCACAAATGCAA--TTTTTTT
* *
5898773 TAAGATCAAGAATAGAAGCAATATAAAGTAATATATTCATTTGTTCAAATTG
129 TAAGATCAAGAACAGAAGCAATATAAAGTAACATATTCATTTGTTCAAATTG
*
5898825 AGGTTGCATCATGTTTTTGTATTCATCAAACAACTCAACTATTGCTTCTTGTACTTTCTTAATCA
1 AGGTTGCATCATGTTTTTGTATTCATCAAACAACTCAACTA-TGCTTCTTGCACTTTCTTAATCA
* *
5898890 TCACTGAAGTTTGATCATGAGAATACATTTTCATAAAGCAAAACTCCACAAATGCAATTTTTTTT
65 TCACTGAAGTTTCATCACGAGAATACATTTTCATAAAGCAAAACTCCACAAATGCAATTTTTTTT
*
5898955 AGGATCAAGAACAGAAGCAATATAAAGTAACATATTCATTT
130 AAGATCAAGAACAGAAGCAATATAAAGTAACATATTCATTT
5898996 TCTCCACATT
Statistics
Matches: 161, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
181 46 0.29
182 40 0.25
183 75 0.47
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (180 bp):
AGGTTGCATCATGTTTTTGTATTCATCAAACAACTCAACTATGCTTCTTGCACTTTCTTAATCAT
CACTGAAGTTTCATCACGAGAATACATTTTCATAAAGCAAAACTCCACAAATGCAATTTTTTTTA
AGATCAAGAACAGAAGCAATATAAAGTAACATATTCATTTGTTCAAATTG
Found at i:5904625 original size:43 final size:44
Alignment explanation
Indices: 5904533--5904657 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 44
5904523 ATGCCAACCT
* * * *
5904533 AAATAATCAAATAAATTGGTACGCATGAAAAATCA-AGATCTACA
1 AAATAAACAAATAAATTAGTACACATGAAAAATCATA-AGCTACA
*
5904577 AAATAAACAAATAAATTAGTACACATAAAAAATCATAAGCTAC-
1 AAATAAACAAATAAATTAGTACACATGAAAAATCATAAGCTACA
** *
5904620 AAATAAACCAAA-AGGTTAGTGCACATGAAAAATCATAA
1 AAATAAA-CAAATAAATTAGTACACATGAAAAATCATAA
5904658 ATAATTACAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
43 29 0.41
44 40 0.57
45 1 0.01
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.21
Consensus pattern (44 bp):
AAATAAACAAATAAATTAGTACACATGAAAAATCATAAGCTACA
Found at i:5905448 original size:13 final size:12
Alignment explanation
Indices: 5905418--5905454 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
5905408 GTATCATAAT
*
5905418 AAATTATGCAAA
1 AAATCATGCAAA
5905430 AAATCATGCAAA
1 AAATCATGCAAA
5905442 AATATCATGCAAA
1 AA-ATCATGCAAA
5905455 TAGAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.22
Consensus pattern (12 bp):
AAATCATGCAAA
Found at i:5905472 original size:20 final size:20
Alignment explanation
Indices: 5905444--5905496 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5905434 CATGCAAAAA
5905444 TATCATGCAAATAGAATAAT
1 TATCATGCAAATAGAATAAT
*
5905464 TATCCTGCAAATAGAATAAT
1 TATCATGCAAATAGAATAAT
*
5905484 AATCATGCAAATA
1 TATCATGCAAATA
5905497 ATAAATCACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.28
Consensus pattern (20 bp):
TATCATGCAAATAGAATAAT
Found at i:5905498 original size:15 final size:16
Alignment explanation
Indices: 5905478--5905513 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5905468 CTGCAAATAG
*
5905478 AATAAT-AATCATGCA
1 AATAATAAATCACGCA
5905493 AATAATAAATCACGCA
1 AATAATAAATCACGCA
5905509 AATAA
1 AATAA
5905514 AATATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AATAATAAATCACGCA
Found at i:5905811 original size:12 final size:13
Alignment explanation
Indices: 5905796--5905827 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5905786 AAAACCAAAC
5905796 AATAAAAAAT-AA
1 AATAAAAAATAAA
5905808 AAT-AAAAATAAA
1 AATAAAAAATAAA
5905820 AATAAAAA
1 AATAAAAA
5905828 CCTTCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 8 0.44
13 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:5907301 original size:6 final size:6
Alignment explanation
Indices: 5907290--5907367 Score: 54
Period size: 6 Copynumber: 13.0 Consensus size: 6
5907280 TACTAACATA
* * * * *
5907290 ATTTTT ATTTTTT ATTTTTAT ATTTTT ATATCT ATTATT ATTATT ATTATT
1 ATTTTT A-TTTTT A-TTTT-T ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
5907341 ATTATT A-TTTT A-TTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
5907368 TATAAATAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
5 14 0.22
6 32 0.51
7 15 0.24
8 2 0.03
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:5907315 original size:15 final size:16
Alignment explanation
Indices: 5907292--5907367 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 16
5907282 CTAACATAAT
5907292 TTTTATTTTT-TATT-
1 TTTTATTTTTATATTA
5907306 TTTATATTTTTATATCTA
1 TTT-TATTTTTATAT-TA
*
5907324 TTATTATTATTATTATTA
1 TT-TTATTTTTA-TATTA
*
5907342 TTATTA-TTTTATTTTA
1 TT-TTATTTTTATATTA
5907358 TTTTATTTTT
1 TTTTATTTTT
5907368 TATAAATAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.06
15 10 0.19
16 13 0.25
17 5 0.10
18 17 0.33
19 4 0.08
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTTTTATATTA
Found at i:5907330 original size:3 final size:3
Alignment explanation
Indices: 5907301--5907364 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
5907291 TTTTTATTTT
* *
5907301 TTA TTT TTA -TA TTT TTA -TA TCTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
5907345 TTA TT- TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
5907365 TTTTATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 10 0.20
3 38 0.75
4 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:5907368 original size:12 final size:12
Alignment explanation
Indices: 5907292--5907370 Score: 63
Period size: 15 Copynumber: 6.1 Consensus size: 12
5907282 CTAACATAAT
5907292 TTTTATTTTTTA
1 TTTTATTTTTTA
5907304 TTTTTATATTTTTA
1 -TTTTAT-TTTTTA
*
5907318 TATCTATTATTATTA
1 T-TTTATT-TT-TTA
5907333 TTATTATTATTATTA
1 TT-TTATT-TT-TTA
5907348 TTTTA--TTTTA
1 TTTTATTTTTTA
5907358 TTTTATTTTTTA
1 TTTTATTTTTTA
5907370 T
1 T
5907371 AAATAATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
10 8 0.14
11 2 0.04
12 6 0.11
13 8 0.14
14 16 0.28
15 17 0.30
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:5907632 original size:29 final size:29
Alignment explanation
Indices: 5907579--5907634 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
5907569 CAATCGTTAT
*
5907579 TTTTTATTAAATATTTTAACTAAATTTTC
1 TTTTTATTAAATATTTTAACAAAATTTTC
5907608 TTTTTATTGAAATATTTTAA-AAAATTT
1 TTTTTATT-AAATATTTTAACAAAATTT
5907635 CTAATACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTATTAAATATTTTAACAAAATTTTC
Found at i:5908422 original size:3 final size:3
Alignment explanation
Indices: 5908401--5908522 Score: 123
Period size: 3 Copynumber: 43.0 Consensus size: 3
5908391 ATCAATTTTC
* * ** *
5908401 ATT ATT GTT ATT ATT -TT ATT A-T ATT ATT GTT AGC A-T AGT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5908445 A-T ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
5908492 ATT ATT ATT ATT -TT -TT ATT GTT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5908523 TTTTTCTTTC
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
2 13 0.13
3 88 0.87
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5909087 original size:32 final size:33
Alignment explanation
Indices: 5909045--5909112 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
5909035 AAATATAAAA
*
5909045 TTTTCAATGAATA-TTTGAA-TTTATCAAT-GAAT
1 TTTTCAATGAA-AGTTTGAACTTT-CCAATCGAAT
*
5909077 TTTTCGATGAAAGTTTGAACTTTCCAATCGAAT
1 TTTTCAATGAAAGTTTGAACTTTCCAATCGAAT
5909110 TTT
1 TTT
5909113 GGCCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 1 0.03
32 20 0.65
33 10 0.32
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (33 bp):
TTTTCAATGAAAGTTTGAACTTTCCAATCGAAT
Found at i:5909395 original size:5 final size:5
Alignment explanation
Indices: 5909387--5909457 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
5909377 ATTTTTTGAC
* * * * *
5909387 TATTT TATTT TATGT TATATT TATTT CATTT TACTT TATTTT TAATT TCTTT
1 TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TA-TTT TATTT TATTT
*
5909439 TA-TT TATAT TA-TT TATTT T
1 TATTT TATTT TATTT TATTT T
5909458 TACTGAATAT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
4 7 0.14
5 35 0.70
6 8 0.16
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:5909411 original size:21 final size:20
Alignment explanation
Indices: 5909387--5909457 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
5909377 ATTTTTTGAC
5909387 TATTTTATTTTATGTTATATT
1 TATTTTATTTTAT-TTATATT
* *
5909408 TATTTCATTTTACTTTATTTT
1 TATTTTATTTTA-TTTATATT
* *
5909429 TAATTTCTTTTATTTATA-T
1 TATTTTATTTTATTTATATT
5909448 TA-TTTATTTT
1 TATTTTATTTT
5909458 TACTGAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
18 7 0.17
19 3 0.07
20 5 0.12
21 26 0.62
22 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (20 bp):
TATTTTATTTTATTTATATT
Found at i:5909443 original size:26 final size:26
Alignment explanation
Indices: 5909387--5909443 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
5909377 ATTTTTTGAC
*
5909387 TATTTTATTTTATGTTATATTTATTT
1 TATTTTACTTTATGTTATATTTATTT
* * *
5909413 CATTTTACTTTAT-TTTTAATTTCTTT
1 TATTTTACTTTATGTTAT-ATTTATTT
5909439 TATTT
1 TATTT
5909444 ATATTATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (26 bp):
TATTTTACTTTATGTTATATTTATTT
Found at i:5909456 original size:22 final size:23
Alignment explanation
Indices: 5909404--5909456 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
5909394 TTTTATGTTA
5909404 TATTTATTTCATTTTACTTTATT
1 TATTTATTTCATTTTACTTTATT
*
5909427 T-TTAATTTC-TTTTA-TTTATAT
1 TATTTATTTCATTTTACTTTAT-T
5909448 TATTTATTT
1 TATTTATTT
5909457 TTACTGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.19
21 7 0.27
22 13 0.50
23 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTATTTCATTTTACTTTATT
Found at i:5914185 original size:12 final size:12
Alignment explanation
Indices: 5914170--5914230 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
5914160 AAGGAAAATT
*
5914170 AAAGTGTAAAAA
1 AAAGTGCAAAAA
5914182 AAAGATGC-AAAA
1 AAAG-TGCAAAAA
5914194 AAA--GCAAAAA
1 AAAGTGCAAAAA
* *
5914204 AAAATGAAAAAA
1 AAAGTGCAAAAA
*
5914216 AAATTGCAAAAA
1 AAAGTGCAAAAA
5914228 AAA
1 AAA
5914231 TTACAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.05
10 7 0.17
12 30 0.73
13 2 0.05
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.10
Consensus pattern (12 bp):
AAAGTGCAAAAA
Found at i:5914202 original size:21 final size:21
Alignment explanation
Indices: 5914177--5914217 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5914167 ATTAAAGTGT
*
5914177 AAAAAAAAGATGCAAAAAAAGC
1 AAAAAAAA-ATGAAAAAAAAGC
5914199 AAAAAAAAATGAAAAAAAA
1 AAAAAAAAATGAAAAAAAA
5914218 ATTGCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAAAAAAATGAAAAAAAAGC
Found at i:5914231 original size:12 final size:12
Alignment explanation
Indices: 5914177--5914244 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 12
5914167 ATTAAAGTGT
5914177 AAAAAAAAGATGC
1 AAAAAAAA-ATGC
5914190 --AAAAAAA-GC
1 AAAAAAAAATGC
5914199 AAAAAAAAATG-
1 AAAAAAAAATGC
5914210 AAAAAAAAATTGC
1 AAAAAAAAA-TGC
* *
5914223 AAAAAAAATTAC
1 AAAAAAAAATGC
5914235 AAAAAGAAAA
1 AAAAA-AAAA
5914245 GAAGAAACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 2 0.04
10 1 0.02
11 22 0.48
12 10 0.22
13 11 0.24
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATGC
Found at i:5915658 original size:3 final size:3
Alignment explanation
Indices: 5915640--5915709 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
5915630 TTTATTAGTC
* * * *
5915640 ATT ATT -TT ATT A-T ATT ATT GTT AGT A-T AGT A-T ATT A-T ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5915683 ATT ATT ATT ATT ATA ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5915710 TTCTTTCTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 10 0.18
3 46 0.82
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5915675 original size:24 final size:25
Alignment explanation
Indices: 5915631--5915709 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 25
5915621 GAATCAATTT
* *
5915631 TTATTAGTCATTATTTTATTATATTA
1 TTATTAGT-ATTAGTATATTATATTA
* *
5915657 TTGTTAGTA-TAGTATATTATACTA
1 TTATTAGTATTAGTATATTATATTA
* * *
5915681 TTATTATTATTATTATAAT-TATTA
1 TTATTAGTATTAGTATATTATATTA
5915705 TTATT
1 TTATT
5915710 TTCTTTCTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 28 0.65
25 8 0.19
26 7 0.16
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (25 bp):
TTATTAGTATTAGTATATTATATTA
Found at i:5916564 original size:5 final size:5
Alignment explanation
Indices: 5916563--5916623 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
5916553 TTTTTTTATT
* * * * *
5916563 TTTTA TTTTA TTTTA TATTTA TTTCA TTATA CTTTA TTTTCA ATTTA TTGTA
1 TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA
5916615 -TTTA TTTTA
1 TTTTA TTTTA
5916624 CTGATTTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
4 3 0.07
5 31 0.72
6 9 0.21
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (5 bp):
TTTTA
Found at i:5918087 original size:12 final size:11
Alignment explanation
Indices: 5918067--5918103 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
5918057 AAAAAAACCT
5918067 TTTATTTTTTA
1 TTTATTTTTTA
*
5918078 TTTAATTTTTTG
1 TTT-ATTTTTTA
5918090 TTTATTTTTTA
1 TTTATTTTTTA
5918101 TTT
1 TTT
5918104 TTATTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:5918233 original size:25 final size:26
Alignment explanation
Indices: 5918185--5918233 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5918175 TAATCATCAT
* **
5918185 TTTTTATTAATTAATTATGGTTAACA
1 TTTTTATTAATAAATTATAATTAACA
5918211 TTTTTA-TAATAAATTATAATTAA
1 TTTTTATTAATAAATTATAATTAA
5918234 TTTAGTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTTATTAATAAATTATAATTAACA
Found at i:5919684 original size:3 final size:3
Alignment explanation
Indices: 5919676--5919709 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5919666 TCTTTCACGT
5919676 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5919710 TTTTCTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5922417 original size:2 final size:2
Alignment explanation
Indices: 5922410--5922447 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5922400 CAAAACTGAT
* *
5922410 GA GA GA GA TA GA GA GA GA TA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5922448 TCAAATGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (2 bp):
GA
Found at i:5922425 original size:10 final size:10
Alignment explanation
Indices: 5922410--5922448 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
5922400 CAAAACTGAT
5922410 GAGAGAGATA
1 GAGAGAGATA
5922420 GAGAGAGATA
1 GAGAGAGATA
*
5922430 GAGAGAGAGA
1 GAGAGAGATA
5922440 GAGAGAGAT
1 GAGAGAGAT
5922449 CAAATGTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.08
Consensus pattern (10 bp):
GAGAGAGATA
Found at i:5927492 original size:47 final size:48
Alignment explanation
Indices: 5927403--5927498 Score: 176
Period size: 47 Copynumber: 2.0 Consensus size: 48
5927393 TGAAATGCGA
5927403 ATTCAATAAATCTAATCCATAAAAAGAGAAATTATAATCGAAATGAAT
1 ATTCAATAAATCTAATCCATAAAAAGAGAAATTATAATCGAAATGAAT
*
5927451 ATTCAATAAATCTAATCGA-AAAAAGAGAAATTATAATCGAAATGAAT
1 ATTCAATAAATCTAATCCATAAAAAGAGAAATTATAATCGAAATGAAT
5927498 A
1 A
5927499 AAACTCCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 29 0.62
48 18 0.38
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.26
Consensus pattern (48 bp):
ATTCAATAAATCTAATCCATAAAAAGAGAAATTATAATCGAAATGAAT
Found at i:5928863 original size:24 final size:25
Alignment explanation
Indices: 5928834--5928887 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
5928824 TGTACTCATT
5928834 AAATATTTATAAAA-ATAAA-ATTAA
1 AAATATTTATAAAATATAAATA-TAA
*
5928858 AAATATTTATTAAATATAAATATAA
1 AAATATTTATAAAATATAAATATAA
5928883 AAATA
1 AAATA
5928888 AAATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.48
25 13 0.48
26 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATATTTATAAAATATAAATATAA
Found at i:5928877 original size:25 final size:24
Alignment explanation
Indices: 5928834--5928887 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
5928824 TGTACTCATT
5928834 AAATATTTATAAAAATAAA-ATTAA
1 AAATATTTATAAAAATAAATA-TAA
*
5928858 AAATATTTATTAAATATAAATATAA
1 AAATATTTA-TAAAAATAAATATAA
5928883 AAATA
1 AAATA
5928888 AAATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.33
25 17 0.63
26 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATATTTATAAAAATAAATATAA
Found at i:5938303 original size:26 final size:23
Alignment explanation
Indices: 5938274--5938323 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 23
5938264 CTGTATATAC
5938274 AAACAAAGAAAAGATGAAAATAGTTT
1 AAACAAAGAAAAG-T-AAAAT-GTTT
*
5938300 AAACAAATAAAAGTAAAATGTTT
1 AAACAAAGAAAAGTAAAATGTTT
5938323 A
1 A
5938324 GATTACAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 5 0.22
25 1 0.04
26 12 0.52
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (23 bp):
AAACAAAGAAAAGTAAAATGTTT
Found at i:5940220 original size:16 final size:16
Alignment explanation
Indices: 5940189--5940218 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5940179 TTTTTTCACT
5940189 GCCATTTTCGACTTTA
1 GCCATTTTCGACTTTA
5940205 GCCA-TTTCGACTTT
1 GCCATTTTCGACTTT
5940219 TATTTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.27, G:0.13, T:0.43
Consensus pattern (16 bp):
GCCATTTTCGACTTTA
Found at i:5940619 original size:12 final size:12
Alignment explanation
Indices: 5940602--5940627 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5940592 CAACTTTATA
5940602 TCTTACATGTTT
1 TCTTACATGTTT
5940614 TCTTACATGTTT
1 TCTTACATGTTT
5940626 TC
1 TC
5940628 CACAAAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (12 bp):
TCTTACATGTTT
Found at i:5948067 original size:22 final size:21
Alignment explanation
Indices: 5948015--5948067 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
5948005 TTTGTAAAAC
5948015 TTATTTTCTCTTTGTTTTATTG
1 TTATTTT-TCTTTGTTTTATTG
*
5948037 TT-TGCTTTTCTTTGCTTTTTTTG
1 TTAT--TTTTCTTTG-TTTTATTG
5948060 TTATTTTT
1 TTATTTTT
5948068 ATGTTTGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
21 1 0.04
22 12 0.46
23 12 0.46
24 1 0.04
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.75
Consensus pattern (21 bp):
TTATTTTTCTTTGTTTTATTG
Found at i:5963474 original size:15 final size:14
Alignment explanation
Indices: 5963454--5963493 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
5963444 TACGATTTTA
5963454 CTTGTTTACTTTCCT
1 CTTGTTTACTTT-CT
*
5963469 CTTGTTTACTTTTT
1 CTTGTTTACTTTCT
5963483 CTT-TTTACTTT
1 CTTGTTTACTTT
5963494 TGTTTAGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 8 0.33
14 4 0.17
15 12 0.50
ACGTcount: A:0.07, C:0.20, G:0.05, T:0.68
Consensus pattern (14 bp):
CTTGTTTACTTTCT
Found at i:5966941 original size:17 final size:17
Alignment explanation
Indices: 5966919--5966951 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5966909 AAAAGCCCAT
5966919 TATTTTATT-TTATTTTA
1 TATTTT-TTGTTATTTTA
5966936 TATTTTTTGTTATTTT
1 TATTTTTTGTTATTTT
5966952 CTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TATTTTTTGTTATTTTA
Found at i:5966966 original size:23 final size:22
Alignment explanation
Indices: 5966923--5966969 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
5966913 GCCCATTATT
* *
5966923 TTATTTTATTTTATATTTTTTG
1 TTATTTTATTTTAAATGTTTTG
*
5966945 TTATTTTCTTTTTAAATGTTTTG
1 TTATTTT-ATTTTAAATGTTTTG
5966968 TT
1 TT
5966970 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (22 bp):
TTATTTTATTTTAAATGTTTTG
Found at i:5968622 original size:23 final size:24
Alignment explanation
Indices: 5968596--5968642 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5968586 TTATTTCAAA
* *
5968596 TAATAAATTTAAGAA-AAAAAGAC
1 TAATAAAATTAAAAATAAAAAGAC
5968619 TAATAAAATTAAAAATAAAAAGAC
1 TAATAAAATTAAAAATAAAAAGAC
5968643 CATTTGGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
TAATAAAATTAAAAATAAAAAGAC
Found at i:5968977 original size:19 final size:19
Alignment explanation
Indices: 5968953--5968989 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5968943 ATAATTTCTA
* *
5968953 ATTTTATTTAATTTTATAT
1 ATTTTATTAAAATTTATAT
5968972 ATTTTATTAAAATTTATA
1 ATTTTATTAAAATTTATA
5968990 AATATTAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATTAAAATTTATAT
Found at i:5972981 original size:26 final size:25
Alignment explanation
Indices: 5972927--5972981 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5972917 CTCACCTAAG
*
5972927 AATTTTATAGAAATTTACCATTTGA
1 AATTTTATAGAAATTTACCATTGGA
* *
5972952 AATTTT-TATAAATTGTATCATTGGA
1 AATTTTATAGAAATT-TACCATTGGA
5972977 TAATT
1 -AATT
5972982 AATATCTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.47
Consensus pattern (25 bp):
AATTTTATAGAAATTTACCATTGGA
Found at i:5973067 original size:27 final size:26
Alignment explanation
Indices: 5973037--5973090 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
5973027 CAAAAAGACT
5973037 AAAAC-ACAAACACATAAATAAAAAAAA
1 AAAACAACAAA-ACATAAA-AAAAAAAA
* *
5973064 AAAACAACAAAATATCAAAAAAAAAA
1 AAAACAACAAAACATAAAAAAAAAAA
5973090 A
1 A
5973091 CGAAACGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 10 0.42
28 5 0.21
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (26 bp):
AAAACAACAAAACATAAAAAAAAAAA
Found at i:5973068 original size:21 final size:22
Alignment explanation
Indices: 5973044--5973091 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
5973034 ACTAAAACAC
5973044 AAAC-ACATAAATA-AAAAAAAA
1 AAACAACA-AAATACAAAAAAAA
5973065 AAACAACAAAATATCAAAAAAAA
1 AAACAACAAAATA-CAAAAAAAA
5973088 AAAC
1 AAAC
5973092 GAAACGGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.08
Consensus pattern (22 bp):
AAACAACAAAATACAAAAAAAA
Done.